3PV8

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.

Wang, W.Hellinga, H.W.Beese, L.S.

(2011) Proc.Natl.Acad.Sci.USA 108: 17644-17648

  • DOI: 10.1073/pnas.1114496108
  • Primary Citation of Related Structures:  
  • Also Cited By: 4F8R, 4F4K, 4F3O, 4F2S, 4F2R, 4EZ9, 4EZ6, 4E0D, 4DSF, 4DQI

  • PubMed Abstract: 
  • Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that c ...

    Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C • A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I
A, D
592Geobacillus kaustophilus (strain HTA426)Mutations: Y426F, A314D
Gene Names: polA
EC: 2.7.7.7
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5KWC1
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')B,E9N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')C,F13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
D3T
Query on D3T

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Download CCD File 
A, D
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2DT
Query on 2DT
B, E
DNA LINKINGC10 H15 N2 O7 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.890α = 90.00
b = 109.300β = 90.00
c = 150.420γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-12-06 
  • Released Date: 2011-10-19 
  • Deposition Author(s): Wang, W., Beese, L.S.

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-11-02
    Type: Database references
  • Version 1.2: 2011-11-09
    Type: Database references
  • Version 1.3: 2017-01-11
    Type: Other